Translation of Gaussian Processes and Step Calculations Fixes
This commit temporarily uses Gaussian Heassian for step calculations, fixes fchk file reading, fixes step calculation, fixes log file and geoms formation. Also this commit adds type hinting to improve and facilitate the program development.
This commit is contained in:
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run.log.backup
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##########################################################################################
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############# Welcome to DICEPLAYER version 1.0 #############
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##########################################################################################
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Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00)
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[GCC 8.4.0]
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Program started on Friday, 03 Dec 2021 at 21:18:49
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Environment variables:
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OMP_STACKSIZE = Not set
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==========================================================================================
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CONTROL variables being used in this run:
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------------------------------------------------------------------------------------------
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altsteps = 20000
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freq = no
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ghosts = no
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initcyc = 1
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lps = no
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maxcyc = 3
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maxstep = 0.3
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nprocs = 4
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opt = yes
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qmprog = g16
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readhessian = no
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switchcyc = 3
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tol_factor = 1.2
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vdwforces = no
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------------------------------------------------------------------------------------------
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DICE variables being used in this run:
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------------------------------------------------------------------------------------------
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combrule = *
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dens = 0.75
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isave = 1000
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ljname = phb.ljc
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ncores = 3
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nmol = 1 50
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nstep = 20000 20000
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outname = phb
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press = 1.0
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progname = dice
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randominit = first
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temp = 300.0
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title = Diceplayer run
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upbuf = 360
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------------------------------------------------------------------------------------------
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GAUSSIAN variables being used in this run:
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------------------------------------------------------------------------------------------
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chgmult = 0 1
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level = MP2/aug-cc-pVTZ
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pop = chelpg
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qmprog = g16
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==========================================================================================
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Program dice found at /usr/local/bin/dice
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Program g16 found at /usr/local/g16/g16
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Program formchk found at /usr/local/g16/formchk
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==========================================================================================
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Potential parameters from file phb.ljc:
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------------------------------------------------------------------------------------------
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Combination rule: *
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Types of molecules: 2
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31 atoms in molecule type 1:
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---------------------------------------------------------------------------------
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Lbl AN X Y Z Charge Epsilon Sigma Mass
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---------------------------------------------------------------------------------
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1 6 -4.40034 0.66551 0.41431 -0.387593 0.07000 3.5500 12.0110
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1 6 -4.49957 -0.67279 -0.15327 0.804001 0.07000 3.5500 12.0110
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1 6 -3.25630 -1.28922 -0.61351 -0.338491 0.07000 3.5500 12.0110
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1 6 -2.05849 -0.66807 -0.48674 -0.220783 0.07000 3.5500 12.0110
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1 6 -1.97114 0.65148 0.10511 0.563527 0.07000 3.5500 12.0110
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1 6 -3.20601 1.29684 0.49712 -0.145372 0.07000 3.5500 12.0110
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2 8 -5.59453 -1.25309 -0.28765 -0.714461 0.21000 2.9600 15.9990
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3 7 -0.87404 1.35870 0.27636 -0.721792 0.17000 3.2500 14.0070
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4 6 0.38785 0.81512 0.14410 0.607123 0.07000 3.5500 12.0110
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4 6 1.40776 1.65800 -0.33261 -0.295476 0.07000 3.5500 12.0110
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4 6 0.75950 -0.46815 0.58791 -0.346661 0.07000 3.5500 12.0110
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4 6 2.71021 1.21519 -0.46119 -0.298546 0.07000 3.5500 12.0110
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4 6 2.07354 -0.89884 0.50831 -0.234284 0.07000 3.5500 12.0110
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4 6 3.08076 -0.08936 -0.06112 0.294651 0.07000 3.5500 12.0110
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5 7 4.37238 -0.53979 -0.20183 -0.190497 0.17000 3.2500 14.0070
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6 6 5.41980 0.43824 -0.43836 -0.213183 0.06600 3.5000 12.0110
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6 6 4.76361 -1.73522 0.52225 -0.225420 0.06600 3.5000 12.0110
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7 1 6.36700 -0.08536 -0.51962 0.109840 0.03000 2.5000 1.0079
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7 1 5.25196 0.96612 -1.37421 0.077140 0.03000 2.5000 1.0079
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7 1 5.49517 1.17412 0.36749 0.125758 0.03000 2.5000 1.0079
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7 1 4.15838 -2.58442 0.21446 0.083229 0.03000 2.5000 1.0079
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7 1 5.79695 -1.96254 0.28041 0.115361 0.03000 2.5000 1.0079
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7 1 4.67416 -1.61707 1.60661 0.121440 0.03000 2.5000 1.0079
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7 1 0.02813 -1.09554 1.08007 0.179434 0.03000 2.4200 1.0079
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7 1 2.31876 -1.86576 0.91913 0.177250 0.03000 2.4200 1.0079
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7 1 3.45102 1.89880 -0.84669 0.198844 0.03000 2.4200 1.0079
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7 1 1.14759 2.66909 -0.61498 0.173388 0.03000 2.4200 1.0079
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7 1 -3.11930 2.29679 0.90060 0.151534 0.03000 2.4200 1.0079
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7 1 -5.31582 1.13611 0.74479 0.205289 0.03000 2.4200 1.0079
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7 1 -3.33813 -2.25037 -1.10231 0.184367 0.03000 2.4200 1.0079
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7 1 -1.16374 -1.11791 -0.89380 0.160382 0.03000 2.4200 1.0079
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16 atoms in molecule type 2:
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---------------------------------------------------------------------------------
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Lbl AN X Y Z Charge Epsilon Sigma Mass
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---------------------------------------------------------------------------------
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1 6 0.67203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110
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1 6 2.07203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110
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1 6 2.76823 -1.61764 0.00263 -0.115000 0.07000 3.5500 12.0110
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1 6 2.06824 -0.40521 0.00264 -0.115000 0.07000 3.5500 12.0110
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1 6 0.67589 -0.40522 0.00264 0.150000 0.07000 3.5500 12.0110
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1 6 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 12.0110
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2 1 0.13203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079
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2 1 2.61203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079
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2 1 2.60824 0.53010 0.00264 0.115000 0.03000 2.4200 1.0079
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2 1 -1.10420 -1.61760 0.00263 0.115000 0.03000 2.4200 1.0079
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3 8 -0.00411 0.77257 0.00264 -0.585000 0.17000 3.0700 15.9990
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3 1 0.61978 1.50220 0.00264 0.435000 0.00000 0.0000 1.0079
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4 6 4.27823 -1.61764 0.00263 0.115000 0.17000 3.8000 12.0110
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4 1 4.63490 -0.74399 0.50704 0.000000 0.00000 0.0000 1.0079
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4 1 4.63490 -2.49130 0.50704 0.000000 0.00000 0.0000 1.0079
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4 1 4.63490 -1.61764 -1.00617 0.000000 0.00000 0.0000 1.0079
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==========================================================================================
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Molecule type 1 - PHENOL_BLUE:
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Center of mass = ( -0.0000 , 0.0000 , 0.0000 )
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Moments of inertia = 3.144054E+02 2.801666E+03 3.027366E+03
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Major principal axis = ( 0.999972 , 0.007210 , 0.002184 )
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Inter principal axis = ( -0.007218 , 0.999967 , 0.003660 )
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Minor principal axis = ( -0.002157 , -0.003676 , 0.999991 )
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Characteristic lengths = ( 11.96 , 5.25 , 2.98 )
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Total mass = 226.28 au
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Total charge = -0.0000 e
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Dipole moment = ( 9.8367 , 0.6848 , 0.8358 ) Total = 9.8959 Debye
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Translating and rotating molecule to standard orientation... Done
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New values:
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Center of mass = ( -0.0000 , -0.0000 , -0.0000 )
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Moments of inertia = 3.144054E+02 2.801666E+03 3.027366E+03
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Major principal axis = ( 1.000000 , 0.000000 , 0.000000 )
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Inter principal axis = ( -0.000000 , 1.000000 , -0.000000 )
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Minor principal axis = ( 0.000000 , 0.000000 , 1.000000 )
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Characteristic lengths = ( 11.97 , 5.27 , 2.99 )
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Total mass = 226.28 au
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Total charge = -0.0000 e
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Dipole moment = ( 9.8432 , 0.6168 , 0.8120 ) Total = 9.8959 Debye
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Molecule type 2 - PLACEHOLDER:
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Center of mass = ( 1.5639 , -1.2534 , 0.0026 )
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Moments of inertia = 1.394830E+02 2.777126E+02 4.141185E+02
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Major principal axis = ( 0.865900 , -0.500217 , -0.000001 )
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Inter principal axis = ( 0.500217 , 0.865900 , 0.000001 )
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Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 )
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Characteristic lengths = ( 5.74 , 5.26 , 1.51 )
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Total mass = 108.14 au
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Total charge = -0.0000 e
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Dipole moment = ( 2.3293 , 0.1593 , -0.0000 ) Total = 2.3347 Debye
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Translating and rotating molecule to standard orientation... Done
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New values:
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Center of mass = ( 0.0000 , -0.0000 , 0.0000 )
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Moments of inertia = 1.394830E+02 2.777126E+02 4.141185E+02
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Major principal axis = ( 1.000000 , -0.000000 , -0.000000 )
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Inter principal axis = ( 0.000000 , 1.000000 , 0.000000 )
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Minor principal axis = ( 0.000000 , -0.000000 , 1.000000 )
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Characteristic lengths = ( 5.65 , 4.95 , 1.51 )
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Total mass = 108.14 au
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Total charge = -0.0000 e
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Dipole moment = ( 1.9373 , 1.3031 , -0.0000 ) Total = 2.3347 Debye
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==========================================================================================
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Starting the iterative process.
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------------------------------------------------------------------------------------------
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Step # 1
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------------------------------------------------------------------------------------------
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Simulation process simfiles/step01/p01 initiated with pid 7513
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p01> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
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Simulation process simfiles/step01/p02 initiated with pid 7514
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p02> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
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Simulation process simfiles/step01/p03 initiated with pid 7515
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p03> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
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Simulation process simfiles/step01/p04 initiated with pid 7516
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p04> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:18:49
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